The manipulation and characterization of residual stress and wafer curvature in anodically bonded structures is useful in improving the reliability of devices built on silicon on glass substrates. Conventional anodic bonding procedures lead to uncontrolled curvature of the bonded substrates as a result of locked-in residual stresses due to thermal expansion mismatch between silicon and Pyrex. A thermomechanical finite element model is used here to elucidate the effect of thermal variations in wafer temperature during anodic bonding. The results inform the development of an anisothermal recipe to control the resulting residual stresses and post bond wafer curvature and to understand the effects of process control on residual curvature. The model suggests that wafer curvature in anodically bonded substrates can be nearly eliminated by reducing the silicon bonding temperature slightly relative to the Pyrex temperature. A simple quantitative model to predict this effect shows promising agreement with experiments.